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10,812 results for “novel”
[Stimulus Set] Evoking the N400 event-related potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)
<p>During speech comprehension, the ongoing context of a sentence is used to predict sentence outcome by limiting subsequent word likelihood. Neurophysiologically, violations of context-dependent predictions result in amplitude modulations of the N400 event-related potential (ERP) component. While N400 is widely used to measure semantic processing and integration, no publicly-available auditory stimulus set is available to standardize approaches across the field. Here, we developed an auditory stimulus set of 442 sentences that utilized the semantic anomaly paradigm, provided cloze probability for all stimuli, and was developed for both children and adults. With 20 neurotypical adults, we validated that this set elicits robust N400's, as well as two additional semantically-related ERP components: the recognition potential (~250 ms) and the late positivity component (~600 ms). This stimulus set (<a href="https://doi.org/10.5061/dryad.9ghx3ffkg">https://doi.org/10.5061/dryad.9ghx3ffkg</a>) and the 20 high-density (128-channel) electrophysiological datasets (<a href="https://doi.org/10.5061/dryad.6wwpzgmx4">https://doi.org/10.5061/dryad.6wwpzgmx4</a>) are made publicly available to promote data sharing and reuse. Future studies that use this stimulus set to investigate sentential semantic comprehension in both control and clinical populations may benefit from the increased comparability and reproducibility within this field of research.</p>
Novel production pathways for the 64Cu / 67Cu theranostic pair through natZn(n, x) reactions
<p>This repository contains all raw gamma-ray spectra analyzed for the present manuscript, as well as calibration spectra. Further details and analysis code are available on reasonable request. </p> <p> </p> <p>The nuclear decay properties of the 64,67Cu radionuclides are favorable for clinical applications, with 64Cu currently being employed for PET imaging. The combined use of 64Cu with 67Cu as a theranostic pair may enable highly personalized therapeutic treatment, with real-time monitoring of dose delivery. In this study, the natZn(n,x) reactions have been investigated as novel production pathways for the 64,67Cu isotopes. The experiment was performed at the Lawrence Berkeley National Laboratory’s 88-Inch Cyclotron, producing fast neutrons through the deuteron breakup process using deuteron beams of 16 MeV and 33 MeV. This study reports spectrum-averaged cross sections for the 64,67Cu isotopes, as well as for 20 additional reaction products from neutron irradiation of natural zinc, zirconium, indium, yttrium and aluminum, more than half of which are measured for the first time. The well-characterized monitor reactions of 89Y(n,2n)88Y, 27Al(n,x)24Na, and natZr(n,x)89Zr were employed to determine the neutron fluence, using the recommendations from the IRDFF-II dosimetry library, and all activities were measured through γ-ray spectroscopy using a high-purity germanium detector. The results are compared to previous experiments from the EXFOR and TENDL-2019 databases, and calculations using ALICE-2017, CoH-3.5.3, EMPIRE-3.2.3, and TALYS-1.9. This work shows that natZn(n,x)64,67Cu is a viable pathway for producing these isotopes, and offers a potential ”tunable” ratio of 64Cu:67Cu for various applications.</p>
Graphic Novel Character Networks and Statistics
<p><strong>Description.</strong> This dataset contains the character networks extracted from the graphic novel Thorgal, as well as the statistics and plots produced when analyzing these networks.</p> <p><strong>Source code. </strong>The source code used to produce these files is available on GitHub: <a href="https://github.com/CompNet/NaNet">https://github.com/CompNet/NaNet</a></p> <p><strong>Citation. </strong>If you use these data, please cite the following article:</p> <ul> <li>V. Labatut, “Complex Network Analysis of a Graphic Novel: The Case of the Bande Dessinée <em>Thorgal</em>,” Advances in Complex Systems, p. 22400033, 2022. ⟨<a href="https://hal.archives-ouvertes.fr/hal-03694768">hal-03694768</a>⟩ - DOI: <a href="http://doi.org/10.1142/S0219525922400033">10.1142/S0219525922400033</a></li> </ul> <p><br><code>@Article{Labatut2022,</code><br><code> author = {Labatut, Vincent},</code><br><code> title = {Complex Network Analysis of a Graphic Novel: The Case of the Bande Dessinée {T}horgal},</code><br><code> journal = {Advances in Complex Systems},</code><br><code> year = {2022},</code><br><code> volume = {25},</code><br><code> number = {5\&6},</code><br><code> pages = {2240003},</code><br><code> doi = {10.1142/S0219525922400033},</code><br><code>}</code></p>
Data and Scripts from: Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa
<p>Morphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Futhermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa, but yields new insights about the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet, but serves as a general framework for predicting multivariate ecology from phenotypic traits.</p>
All-atom molecular dynamics simulations of phenylalanine-4-hydroxylase (PAH) tetramer to investigate the impact of two novel heterozygous mutations, p.Y198N and p.Y204F, observed in a classical phenylketonuria patient
<p>Phenylalanine-4-hydroxylase (PAH) tetramer system (Robetta modelling to complete the structure with template PDB ID: 6hyc) with parametrised BH<sub>4</sub> ligand (parameters are available in the dataset) and Fe(II) metal ions in a TIP3P water box ionised with 0.15 M KCl were presented as wild-type and carrying two novel mutations as Y198N on dimeric chains A and B, and Y204F on dimeric chains C and D. In addition, E353 and E422 are protonated as predicted by PROPKA. BH<sub>4</sub> molecule parametrization was performed by using GAFF, Antechamber and “amb2chm_par.py” program of Amber2018.</p> <p>5,000-step minimization and 1 ns equilibration were performed by fixing the protein to relax the system. Then, another 5,000-step minimization and 1 ns equilibration were performed without any constraints, except the SHAKE algorithm on water molecules, to relax the protein and system. The production simulations were performed along 100 ns trajectory at 310 K collected under NpT ensemble.</p> <p>All system preparation and simulation details for this dataset is available with the related background, results and conclusions in the following article:</p> <p>Tolga Aslan, Aslı Yenenler-Kutlu, Umut Gerlevik, Ayşe Çiğdem Aktuğlu Zeybek, Ertuğrul Kıykım, Osman Uğur Sezerman & Necla Birgul Iyison (2021) Identifying and elucidating the roles of Y198N and Y204F mutations in the PAH enzyme through molecular dynamic simulations, Journal of Biomolecular Structure and Dynamics, DOI: <a href="https://doi.org/10.1080/07391102.2021.1921619">10.1080/07391102.2021.1921619</a></p>
Fig. 3. Candolleomyces asiaticus M.Asif, A in Candolleomyces asiaticus sp. nov. (Psathyrellaceae, Agaricales), a novel species from Punjab, Pakistan
Fig. 3. Candolleomyces asiaticus M.Asif, A.Izhar, Niazi & Khalid sp. nov., holotype (LAH36809), line drawings. A. Basidia. B. Basidiospores. C. Cheilocystidia. D. Pileipellis. E. Stipitipellis hyphae. Scale bars: A–C = 5 µm; D–E = 20 µm. Drawings by Aiman Izhar.
Fig. 2. Candolleomyces asiaticus M.Asif, A in Candolleomyces asiaticus sp. nov. (Psathyrellaceae, Agaricales), a novel species from Punjab, Pakistan
Fig. 2. Candolleomyces asiaticus M.Asif, A.Izhar, Niazi & Khalid sp. nov., holotype (LAH36809). Basidiomata. Photos by Muhammad Asif & Aiman Izhar.
Fig. 1 in Candolleomyces asiaticus sp. nov. (Psathyrellaceae, Agaricales), a novel species from Punjab, Pakistan
Fig. 1. Molecular phylogenetic placement of Candolleomyces asiaticus M.Asif, A.Izhar, Niazi & Khalid sp. nov. based on maximum likelihood (ML) method of nrITS sequences.
Dataset Practical Performance and User Experience of Novel DUAL-Flush Vacuum Toilets
<p>Dataset for paper "Practical Performance and User Experience of Novel DUAL-Flush Vacuum Toilets" <a href="https://doi.org/10.3390/w13162228">https://doi.org/10.3390/w13162228</a> <em>Water</em> <strong>2021</strong>, <em>13</em>(16), 2228</p> <p> </p>
References extracted from an archived version of the hyperfiction novel "The Unknown"
<p>This repository contains reference data extracted from an archived version of the hyperfiction novel "The Unknown". [1] Archiving was done with `wget`, data was written to a WARC file. We can't provide the WARC file here due to copyright reasons, but we're happy to provide the WARC file upon request, e.g. if you want to reproduce our findings starting from the original WARC.</p> <p>All reference data has been extracted using warc2graph, a Python package available via the Python Package Index and on Github: <a href="https://github.com/dla-marbach/warc2graph/">https://github.com/dla-marbach/warc2graph/</a> . This software is under development, extraction for this study was done with <a href="https://pypi.org/project/warc2graph/0.1.1/">version 0.1.1</a>.</p> <p>We use the term reference data as warc2graph extracts more information than what is defined as a link in the HTML 5 specification. For more info about the data model see <a href="https://elmcip.net/node/16380">(Schlesinger, Blessing, Hein, Ulrich 2021)</a>. [2]</p> <p>We provide the following files, which are all derivatives of the original WARC file. Gephi files contain layout decisions and reduced data according to our research question and as presented in our presentation of this study at <a href="https://dh2022.adho.org/">DH 2022</a>.</p> <ul> <li><strong>extracted-references.complete.the-unknown.hypertext-novel.gexf</strong>: full reference data extracted with warc2graph in GEXF format.</li> <li><strong>extracted-references.internal-only.the-unknown.hypertext-novel.gephi</strong>: internal links only (= no links pointing to sites other than unknownhypertext.com), Gephi format.</li> <li><strong>extracted-references.internal-only.no-navigation.the-unknown.hypertext.novel.gephi</strong>: internal links only, minus nodes that mirror the navigation menu on the bottom of very many pages, Gephi format.</li> <li><strong>external_links</strong>: list of outgoing links, plain text format</li> </ul> <p> </p> <p>[1] Gillespie, William, Scott Rettberg, and Dirk Stratton. ‘The Unknown’, 2002 1998. <a href="https://unknownhypertext.com/">https://unknownhypertext.com/</a>.</p> <p>[2] Schlesinger, Claus-Michael, Mona Ulrich, André Blessing, and Pascal Hein. ‘Networks of Net Literature - Modelling, Extracting and Visualizing Link-Based Networks in the DLA Corpus of Net Literature’. Bergen: ELMCIP, 2021. https://elmcip.net/node/16380.</p>
Novel host plant unmasks heritable variation in plant preference within an insect population
<p>Introductions of novel plant species can disturb the historical resource environment of herbivorous insects, resulting in strong selection to either adopt or exclude the novel host. However, an adaptive response depends on heritable genetic variation for preference or performance within the targeted herbivore population, and it is unclear how heritability of host-use preference may differ between novel and historical hosts. <em>Pieris macdunnoughii</em> butterflies in the Rocky Mountains lay eggs on the nonnative mustard <em>Thlaspi arvense</em>, which is lethal to their offspring. Heritability analyses revealed considerable sex-linked additive genetic variation in host preference within a population of this butterfly. This was contrary to general predictions about the genetic basis of preference variation, which are hypothesized to be sex-linked between populations but autosomal within populations. Evidence of sex-linkage disappeared when butterflies were tested on methanol-based chemical extracts, suggesting these chemicals in isolation may not be the primary driver of female choice among available host plants. Although unexpected, evidence for within-population sex-linked genetic variation in preference for <em>T. arvense</em> over native hosts indicates that persistent maladaptive oviposition on this lethal plant must be maintained by alternative evolutionary dynamics such as migration- or drift-selection balance or pleiotropic constraints.</p>
Data from: A novel laboratory method to simulate climatic stress with successful application to experiments with medically relevant ticks
<p>Ticks are the most important vectors of zoonotic disease-causing pathogens in North America and Europe. Many tick species are expanding their geographic range. Although correlational evidence suggests that climate change is driving the range expansion of ticks, experimental evidence is necessary to develop a mechanistic understanding of ticks' response to a range of climatic conditions. Previous experiments used simulated microclimates, but these protocols require hazardous salts or expensive laboratory equipment to manipulate humidity. We developed a novel, safe, stable, convenient, and economical method to isolate individual ticks and manipulate their microclimates. The protocol involves placing individual ticks in plastic tubes, and placing six tubes along with a commercial two-way humidity control pack in an airtight container. We successfully used this method to investigate how humidity affects survival and host-seeking (questing) behavior of three tick species: the lone star tick (Amblyomma americanum), American dog tick (Dermacentor variabilis), and black-legged tick (Ixodes scapularis). We placed 72 adult females of each species individually into plastic tubes and separated them into three experimental relative humidity (RH) treatments representing distinct climates: 32% RH, 58% RH, and 84% RH. We assessed the survival and questing behavior of each tick for 30 days. In all three species, survivorship significantly declined in drier conditions. Questing height was negatively associated with RH in Amblyomma, positively associated with RH in Dermacentor, and not associated with RH in Ixodes. The frequency of questing behavior increased significantly with drier conditions for Dermacentor but not for Amblyomma or Ixodes. This report demonstrates an effective method for assessing the viability and host-seeking behavior of tick vectors of zoonotic diseases under different climatic conditions.</p>
Data for Novel Approach to Quantify Sediment Transfer and Storage in Rivers with Feldspar Single-Grain pIRIR
<p>Raw data of feldspar post infra-red infra-red (pIRIR) stimulated luminescence signal from modern sand from New Zealand rivers (Rakaia, six samples; Waimakariri, height samples) used in the paper Guyez et al. (2022) submitted to JGR: Earth Surface. The samples were collected in February 2020 by S. Bonnet and A. Guyez. They were measured in the Netherlands Center for Luminescence dating (Wageningen University and Research). </p>
Evoking the N400 Event-Related Potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)
<p class="MsoNoSpacing"><span>During speech comprehension, the ongoing context of a sentence is used to predict sentence outcome by limiting subsequent word likelihood. Neurophysiologically, violations of context-dependent predictions result in amplitude modulations of the N400 event-related potential (ERP) component. While N400 is widely used to measure semantic processing and integration, </span><span>no publicly-available auditory stimulus set is available to standardize approaches across the field. Here, we developed an auditory stimulus set of 442 sentences that utilized the semantic anomaly paradigm, provided cloze probability for all stimuli, and was developed for both children and adults. With 20 neurotypical adults, we validated that this set elicits robust N400's, as well as two additional semantically-related ERP components: the recognition potential (~250 ms) and the late positivity component (~600 ms). This stimulus set (<a href="https://doi.org/10.5061/dryad.9ghx3ffkg">https://doi.org/10.5061/dryad.9ghx3ffkg</a>) and the 20 high-density (128-channel) electrophysiological datasets (<a href="https://doi.org/10.5061/dryad.6wwpzgmx4">https://doi.org/10.5061/dryad.6wwpzgmx4</a>) </span><span>are made publicly available to promote data sharing and reuse. Future studies that use this stimulus set to investigate sentential semantic comprehension in both control and clinical populations may benefit from the increased comparability and reproducibility within this field of research.</span></p>
Accompanying data - UnCorrupt SMILES: a novel approach to de novo design
<p>This repository contains the files used for "UnCorrupt SMILES: a novel approach to de novo design".</p>
Data from: Andriollo T., Ruedi M. (2018). Novel molecular tools to identify Plecotus bats in sympatry and a review of their distribution in Switzerland. Revue suisse de Zoologie 125(1)
<p><strong>Supporting data for:</strong> Andriollo T., Ruedi M. (2018). Novel molecular tools to identify <em>Plecotus</em> bats in sympatry. Revue suisse de Zoologie 125(1): 61-72. https://doi.org/10.5281/zenodo.1196013</p>
Dogs do not use their own experience with novel barriers to infer others' visual access
<p>Despite extensive research into the Theory of Mind abilities in nonhuman animals, it remains controversial whether they can attribute mental states to other individuals or whether they merely predict future behaviour based on previous behavioural cues. In the present study, we tested pet dogs (in total, N=92) on adaptations of the "goggles test" previously used with human infants and great apes. In both a cooperative and a competitive task, dogs were given direct experience with the properties of novel screens (one opaque, the other transparent) inserted into identical, but differently coloured, tunnels. Dogs learned and remembered the properties of the screens even when, later on, these were no longer directly visible to them. Nevertheless, they were not more likely to follow the experimenter's gaze to a target object when the experimenter could see it through the transparent screen. Further, they did not prefer to steal a forbidden treat first in a location obstructed from the experimenter's view by the opaque screen. Therefore, dogs did not show perspective-taking abilities in this study in which the only available cue to infer others' visual access consisted of the subjects' own previous experience with novel visual barriers. We conclude that the behaviour of our dogs, unlike that of infants and apes in previous studies, does not show evidence of experience projection abilities.</p>
Single-cell profiling reveals immune-based mechanisms underlying tumor radiosensitization by a novel Mn porphyrin clinical candidate, MnTnBuOE-2-PyP5+ (BMX-001)
<p>Manganese porphyrins reportedly exhibit synergic effects when combined with irradiation. However, an in-depth understanding of intratumoral heterogeneity and immune pathways, as affected by Mn porphyrins, remains limited. Here, we explored the mechanisms underlying immunomodulation of a clinical candidate, MnTnBuOE-2-PyP<sup>5+</sup> (BMX-001, MnBuOE), using single-cell analysis in murine carcinoma<em> </em>model. Mice bearing 4T1 tumors were divided into 4 groups: control, MnBuOE, radiotherapy (RT), combined MnBuOE, and radiotherapy (MnBuOE/RT). In epithelial cells, epithelial-mesenchymal transition, TNF-α signaling via NF-кB, angiogenesis, and hypoxia-related genes were significantly downregulated in the MnBuOE/RT compared to the RT. All subtypes of cancer-associated fibroblasts (CAFs) were reduced in MnBuOE and MnBuOE/RT. Inhibitory receptor-ligand interactions, in which epithelial cells and CAFs interacted with CD8+ T cells, were significantly lower in the MnBuOE/RT than in the RT. Trajectory analysis showed that DC maturation-associated markers were increased in MnBuOE/RT. M1 macrophages were significantly increased in the MnBuOE/RT compared to the RT, whereas myeloid-derived suppressor cells were decreased. CellChat analysis showed that the number of cell-cell communications was the lowest in the MnBuOE/RT. Our study is the first to provide evidence for the combined radiotherapy with a novel Mn porphyrin clinical candidate, BMX-001 from the perspective of each cell type within the tumor microenvironment.</p>
Data and Analysis Scripts for "Diviner uncovers hundreds of novel human (and other) exons through comparative analysis of proteins"
<p>This compressed directory contains the complete set of data and analysis scripts represented in "<em>Diviner</em> uncovers novel coding regions on eukaryotic genomes using targeted homology search."</p> <p> </p>
A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments: Supporting Data
<p>Experimental data including Excel analysis and microscopy supporting the publication 'A novel flow chamber for biodegradable alloy assessment in physiologically realistic environments' <a href="https://doi.org/10.1063/1.4821498" target="_blank" rel="noopener">https://doi.org/10.1063/1.4821498</a></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.